the WT SARS-CoV-2 in cell-based models and
in a rhesus monkey model ( 20 ). JMB2002 has
completed a phase 1 clinical trial in healthy
donors and was shown to have excellent safety
and pharmacokinetic properties and has been
approved for a clinical trial in the United
States (IND 154745). We evaluated the binding
of JMB2002 to WT and Omicron spike trimers.
JMB2002 Fab bound the Omicron spike trimer
with approximately fourfold increased affinity
(KD= 3.2 ± 3.0 nM) compared with the WT
spike trimer (KD= 12.2 ± 11.6 nM), whereas
JMB2002 IgG showed similar avidity for the
Omicron spike trimer (KD= 0.4 ± 0.1 nM)
and WT (KD= 0.5 ± 0.3 nM) (Fig. 4, A to D).
Furthermore, JMB2002 was able to directly
inhibit the binding of ACE2 to the Omicron
spike trimer with a median inhibitory con-
centration of 1.8 nM (Fig. 4E). In pseudovirus
neutralization assays, JMB2002 effectively
blocked the entry of the Omicron pseudovirus
into human ACE2-expressing cells in addition
to blocking the WT pseudovirus (Fig. 4F and
fig. S6A). JMB2002 was also able to neutral-
ize a number of VOCs, including variants of
Alpha, Beta, and Gamma, but not Delta (fig.
S6, B to E).
To reveal the basis of JMB2002 inhibition
of Omicron, we solved the structure of the
Omicron spike trimer bound to a Fab from
JMB2002 at a global resolution of 2.69 Å
(Fig. 5A, table S1, and figs. S7 and S8). To
stabilize the constant regions of Fab, we used
a nanobody that binds to the interface be-
tween the variable and constant regions of
the light chain ( 21 ). The cryo–electron micro-
scopy(cryo-EM)densitymaprevealsthebind-
ing of two Fab molecules to two RBDs (one up
and one down) of the trimeric spike (Fig. 5,
A and B). The overall structure of the spike
trimer in the Fab-bound complex is very
similar to that of the ACE2-bound complex,
with a root mean square difference of 1.0 Å
over all Caatoms of the spike trimer, including
the unusual RBD-RBD dimer configuration
(fig. S9, A and B).
Within the Fab-spike trimer structure, both
Fabs bind to the same region in their re-
spective RBD (Fig. 5, C and D). Local refine-
ment of the Fab-bound RBD structure generated
a density map to a resolution of 2.47 Å (figs. S7G
and S8D), which provides detailed interac-
tions between Fab and RBD. The Fab-binding
site does not overlap with the ACE2-binding
site (fig. S9C). However, in the context of the
trimer, Fab binding to the down RBD would
clash with ACE2 binding to the up RBD (Fig.
5E), consistent with direct inhibition of
ACE2 binding to the Omicron spike trimer
by JMB2002 (Fig. 4E).
Particle classification also revealed two ad-
ditional antibody-bound complexes at a global
resolution of 2.92 and 3.18 Å, respectively (figs.
S7 and S8). One of the two complexes has the
spike trimer with one up RBD bound to one
Fab and two down RBDs in the apo state (fig.
S8A). The other complex contains the spike
trimer with two up RBDs and one down RBD,
with each RBD bound to one Fab (fig. S8C).
The up-down RBD-RBD interactions within
the spike trimer are conserved in these com-
plexes. The diverse configuration and stoichi-
ometry ratio of the spike trimer bound to the
antibody further highlight the conformation
flexibility of the Omicron spike RBD. The ability
of the spike trimer to bind to three Fab mole-
cules provides additional evidence for the poten-
cy of JMB2002 against Omicron.
The L452R mutation in the Delta variant is
at the center of the binding epitope of JMB2002,
and this mutation would clash with Y102 from
the heavy chain of the Fab (Fig. 5F), thus pro-viding an explanation for its loss of potency
against the Delta variant. In addition, the bind-
ing site of the JMB2002 Fab on the RBD is
distinct from the epitopes for previously de-
fined class I to class IV antibodies (Fig. 5G)
( 22 ), so JMB2002 represents a new class of
antibody against the spike trimer.
In this study, we report biochemical char-
acterization of the Omicron spike trimer and
its binding to ACE2. Our data reveal that the
Omicron RBD is less stable and more dynamic
than the WT RBD, and the Omicron spike trimer
has sixfold to ninefold increased affinity for bind-
ing to ACE2. We further solved the structures
of the Omicron spike trimer in the apo state or
boundtoACE2orananti-Omicronantibody.
The ACE2-bound structure reveals that the
Omicron spike trimer contains an unusualSCIENCEscience.org 4 MARCH 2022•VOL 375 ISSUE 6584 1051
0.001 0.01 0.1 1 10 100-50050100Neutralization against OmicronAntibody concentration (g/ml)Neutralization (%)JMB2002 = 0.15 ± 0.08
Control IgG > 100IC 50 (g/ml)A BC DE FInhibition %-12 -11 -10 -9 -8 -7050100150JMB2002 blocks ACE2 binding Omicron S ECDLog [Antibody] MControl IgG > 30 nMJMB2002 = 1.8 nMIC 50 ( nM)0 200 4000.000.050.100.150.20JMB2002 Fab binding with Omicron S ECDTime (s)Binding (nm)KD=3.2 3.0 nM55.6 nM
18.5 nM
6.17 nM
2.06 nM0 100 200 300 400 5000.00.10.20.30.40.5JMB2002 IgG binding with Omicron S ECDTime (s)Binding(nm)KD=0.4 0.1 nM0 100 200 300 400 5000.000.050.100.150.200.25JMB2002 Fab binding with WT S ECDTime (s)Binding (nm)KD=12.2 11.6 nM0 100 200 300 400 5000.00.20.40.6JMB2002 IgG binding with WT S ECDTime (s)Binding (nm)KD=0.5 0.3 nMFig. 4. Inhibition of ACE2 binding to the spike trimer by an anti-Omicron antibody.(AandC) Binding
of JMB2002 Fab to the Omicron and WT spike trimer. (BandD) Binding of JMB2002 IgG to the Omicron and
WT spike trimer. (E) Direct inhibition of ACE2 binding to the Omicron spike trimer by JMB2002. (F) Inhibition
of the pseudovirus of Omicron by JMB2002.RESEARCH | REPORTS